The story...

Throughout the 1990s, the Pakistan Inter Services Intelligence (ISI) was used by the CIA as a go-between -- to channel weapons and Mujahideen mercenaries to the Bosnian Muslim Army in the civil war in Yugoslavia. According to a report of the London based International Media Corporation:
Osamagate
Michel Chossudovsky
http://globalresearch.ca/articles/CHO110A.html

Our take...

Chossudovsky uses this quote as support for his claim:

  "Reliable sources report that the United States is now [1994] actively participating in the arming and training of the Muslim forces of Bosnia-Herzegovina in direct contravention of the United Nations accords. US agencies have been providing weapons made in ... China (PRC), North Korea (DPRK) and Iran. The sources indicated that ... Iran, with the knowledge and agreement of the US Government, supplied the Bosnian forces with a large number of multiple rocket launchers and a large quantity of ammunition. These included 107mm and 122mm rockets from the PRC, and VBR-230 multiple rocket launchers ... made in Iran. ... It was [also] reported that 400 members of the Iranian Revolutionary Guard (Pasdaran) arrived in Bosnia with a large supply of arms and ammunition. It was alleged that the US Central Intelligence Agency (CIA) had full knowledge of the operation and that the CIA believed that some of the 400 had been detached for future terrorist operations in Western Europe.

  During September and October [1994], there has been a stream of "Afghan" Mujahedin ... covertly landed in Ploce, Croatia (South-West of Mostar) from where they have traveled with false papers ... before deploying with the Bosnian Muslim forces in the Kupres, Zenica and Banja Luka areas. These forces have recently [late 1994] experienced a significant degree of military success. They have, according to sources in Sarajevo, been aided by the UNPROFOR Bangladesh battalion, which took over from a French battalion early in September [1994].

  The Mujahedin landing at Ploce are reported to have been accompanied by US Special Forces equipped with high-tech communications equipment, ... The sources said that the mission of the US troops was to establish a command, control, communications and intelligence network to coordinate and support Bosnian Muslim offensives -- in concert with Mujahideen and Bosnian Croat forces -- in Kupres, Zenica and Banja Luka. Some offensives have recently been conducted from within the UN-established safe-havens in the Zenica and Banja Luka regions.

  (...)

  The US Administration has not restricted its involvement to the clandestine contravention of the UN arms embargo on the region ... It [also] committed three high-ranking delegations over the past two years [prior to 1994] in failed attempts to bring the Yugoslav Government into line with US policy. Yugoslavia is the only state in the region to have failed to acquiesce to US pressure.
http://globalresearch.ca/articles/CHO110A.html

Read this carefully and you’ll note there’s nothing here about Pakistan, the ISI or CIA. Are we to assume that the "stream of "Afghan" Mujahedin" can only have been supplied by Pakistan? If so, a paragraph from the original International Media Corporation article suggests that isn’t true:

The "Afghan" mujahedin are not all veterans of the Afghan war: the 3,000 or so of this force around the Zenica area are drawn mainly from Malaysia, Pakistan, Iran, and Turkey. They are fighting as part of the Bosnian Muslim 3rd Corps, deployed at Zenica and in the nearby villages of Arnauti, Nemill, Bistricak, Stranjani, Mehuric, Janjici, and Kasapouici. As well, housed on the top floor of the most important hotel in Zenica are 30 Iranian military instructors engaged in training Bosnian Muslim forces and specialist terrorist (or special operations) units.
http://www.angelfire.com/in/beograd/dfa53.html

Some from Pakistan, then, but still no mention of the ISI. And definitely no support for the original statement. In fact it seems that Iran was far more involved with this affair than Pakistan. Does that mean they should now be viewed as subservient to the CIA? Or could it be that drawing long-term conclusions from a report relating primarily to events in September and October 1994, is just a little simplistic?

None of this means the Pentagon or US were innocent, of course, as Dutch Professor Cees Wiebes pointed out in 2002:

America used Islamists to arm the Bosnian Muslims

The Srebrenica report reveals the Pentagon's role in a dirty war

Richard J Aldrich
Monday April 22, 2002
The Guardian

The official Dutch inquiry into the 1995 Srebrenica massacre, released last week, contains one of the most sensational reports on western intelligence ever published. Officials have been staggered by its findings and the Dutch government has resigned. One of its many volumes is devoted to clandestine activities during the Bosnian war of the early 1990s. For five years, Professor Cees Wiebes of Amsterdam University has had unrestricted access to Dutch intelligence files and has stalked the corridors of secret service headquarters in western capitals, as well as in Bosnia, asking questions.

His findings are set out in "Intelligence and the war in Bosnia, 1992-1995". It includes remarkable material on covert operations, signals interception, human agents and double-crossing by dozens of agencies in one of dirtiest wars of the new world disorder. Now we have the full story of the secret alliance between the Pentagon and radical Islamist groups from the Middle East designed to assist the Bosnian Muslims - some of the same groups that the Pentagon is now fighting in "the war against terrorism". Pentagon operations in Bosnia have delivered their own "blowback".

In the 1980s Washington's secret services had assisted Saddam Hussein in his war against Iran. Then, in 1990, the US fought him in the Gulf. In both Afghanistan and the Gulf, the Pentagon had incurred debts to Islamist groups and their Middle Eastern sponsors. By 1993 these groups, many supported by Iran and Saudi Arabia, were anxious to help Bosnian Muslims fighting in the former Yugoslavia and called in their debts with the Americans. Bill Clinton and the Pentagon were keen to be seen as creditworthy and repaid in the form of an Iran-Contra style operation - in flagrant violation of the UN security council arms embargo against all combatants in the former Yugoslavia.

The result was a vast secret conduit of weapons smuggling though Croatia. This was arranged by the clandestine agencies of the US, Turkey and Iran, together with a range of radical Islamist groups, including Afghan mojahedin and the pro-Iranian Hizbullah. Wiebes reveals that the British intelligence services obtained documents early on in the Bosnian war proving that Iran was making direct deliveries.

Arms purchased by Iran and Turkey with the financial backing of Saudi Arabia made their way by night from the Middle East. Initially aircraft from Iran Air were used, but as the volume increased they were joined by a mysterious fleet of black C-130 Hercules aircraft. The report stresses that the US was "very closely involved" in the airlift. Mojahedin fighters were also flown in, but they were reserved as shock troops for especially hazardous operations.

Light weapons are the familiar currency of secret services seeking to influence such conflicts. The volume of weapons flown into Croatia was enormous, partly because of a steep Croatian "transit tax". Croatian forces creamed off between 20% and 50% of the arms. The report stresses that this entire trade was clearly illicit. The Croats themselves also obtained massive quantities of illegal weapons from Germany, Belgium and Argentina - again in contravention of the UN arms embargo. The German secret services were fully aware of the trade.

Rather than the CIA, the Pentagon's own secret service was the hidden force behind these operations. The UN protection force, UNPROFOR, was dependent on its troop-contributing nations for intelligence, and above all on the sophisticated monitoring capabilities of the US to police the arms embargo. This gave the Pentagon the ability to manipulate the embargo at will: ensuring that American Awacs aircraft covered crucial areas and were able to turn a blind eye to the frequent nightime comings and goings at Tuzla.

Weapons flown in during the spring of 1995 were to turn up only a fortnight later in the besieged and demilitarised enclave at Srebrenica. When these shipments were noticed, Americans pressured UNPROFOR to rewrite reports, and when Norwegian officials protested about the flights, they were reportedly threatened into silence.

Both the CIA and British SIS had a more sophisticated perspective on the conflict than the Pentagon, insisting that no side had clean hands and arguing for caution. James Woolsey, director of the CIA until May 1995, had increasingly found himself out of step with the Clinton White House over his reluctance to develop close relations with the Islamists. The sentiments were reciprocated. In the spring of 1995, when the CIA sent its first head of station to Sarajevo to liaise with Bosnia's security authorities, the Bosnians tipped off Iranian intelligence. The CIA learned that the Iranians had targeted him for liquidation and quickly withdrew him.

Iranian and Afghan veterans' training camps had also been identified in Bosnia. Later, in the Dayton Accords of November 1995, the stipulation appeared that all foreign forces be withdrawn. This was a deliberate attempt to cleanse Bosnia of Iranian-run training camps. The CIA's main opponents in Bosnia were now the mojahedin fighters and their Iranian trainers - whom the Pentagon had been helping to supply months earlier.

Meanwhile, the secret services of Ukraine, Greece and Israel were busy arming the Bosnian Serbs. Mossad was especially active and concluded a deal with the Bosnian Serbs at Pale involving a substantial supply of artillery shells and mortar bombs. In return they secured safe passage for the Jewish population out of the besieged town of Sarajevo. Subsequently, the remaining population was perplexed to find that unexploded mortar bombs landing in Sarajevo sometimes had Hebrew markings.

The broader lessons of the intelligence report on Srebrenica are clear. Those who were able to deploy intelligence power, including the Americans and their enemies, the Bosnian Serbs, were both able to get their way. Conversely, the UN and the Dutch government were "deprived of the means and capacity for obtaining intelligence" for the Srebrenica deployment, helping to explain why they blundered in, and contributed to the terrible events there.

Secret intelligence techniques can be war-winning and life-saving. But they are not being properly applied. How the UN can have good intelligence in the context of multinational peace operations is a vexing question. Removing light weapons from a conflict can be crucial to drawing it down. But the secret services of some states - including Israel and Iran - continue to be a major source of covert supply, pouring petrol on the flames of already bitter conflicts.
http://www.guardian.co.uk/comment/story/0,3604,688310,00.html

In this version of the story we have talk of the CIAs "reluctance to develop close relations with the Islamists". There certainly was contact through the Pentagon and intermediaries like Iran, but how involved were they with members of terrorist groups who fought in the Balkans?. Even some books with sympathy for 9/11 “inside job” theories hesitate to offer a definitive answer (our emphasis):

For a detailed analysis of US involvement in the covert arms “pipeline” to Bosnia, see Cees Wiebes, Intelligence and the War in Bosnia, 1992-1995, James Bennett, 2003, pp. 157-213. According to Wiebes’s painstaking research, a number of proscribed international “terrorist” organisations also supplied volunteers to fight alongside the Bosnian army as “shock troops”, including Hamas, Hezbollah and the Algerian FIS. Whether Pentagon officials who provided assistance to the Bosnian Muslims sanctioned or assisted such participation is not clear. But such apparently improbable alliances were not uncommon in the twilight world of covert operations, which were generally informed by a logic and set of ethical standards very different from those proclaimed in the official anti-terrorist anathema, even if the Western public was not aware of the discrepancy.

Footnote #17 to Chapter 11
Page 350
Unknown Soldiers
Matthew Carr

So it’s “not clear” that the US sanctioned the involvement of any proscribed organisation, at least according to this analysis. And with regard to the original claim, there’s once more nothing at all on the CIA using the ISI as a go-between: no support at all..